Sounds like it's time to break out the scope
Tracing waveforms can get you a good idea of where the problem lies. Do you have a reference of what they should look like? (Usually in a Sam's)
Also, if you have substitute tubes, it may be worth trying those too. Some sets drive them to their design limits, and the result is a set that works perfectly with one tube, but not another that is slightly out of spec. Both tubes will still test good, of course, so the easiest way to find this problem is what's called the "tube roll" (swapping tubes in the problem areas with another one).